In a method of manufacturing a semiconductor device, in order to remove deposits adhering to a surface, cleaning has conventionally been performed. For example, a technique disclosed in Japanese Patent Laying-Open No. 6-314679 (PTL 1) is exemplified as such a cleaning method. The method of cleaning a semiconductor substrate in PTL 1 is performed in the following manner. Initially, a silicon (Si) substrate is cleaned with ultrapure water containing ozone to thereby form an Si oxide film, so that particles and a metal impurity are taken into the inside or into a surface of this Si oxide film. Then, this Si substrate is cleaned with a diluted hydrofluoric acid aqueous solution so that the Si oxide film is etched away and simultaneously the particles and the metal impurity are removed.